Alignments for a candidate for metX in Sphingomonas koreensis DSMZ 15582

GapMind for Amino acid biosynthesis

Alignments for a candidate for metX in Sphingomonas koreensis DSMZ 15582

Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate Ga0059261_2301 Ga0059261_2301 homoserine O-acetyltransferase (EC 2.3.1.31)

Query= SwissProt::Q9AAS1
         (382 letters)



>FitnessBrowser__Korea:Ga0059261_2301
          Length = 371

 Score =  493 bits (1270), Expect = e-144
 Identities = 238/352 (67%), Positives = 282/352 (80%), Gaps = 3/352 (0%)

Query: 22  PLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKPGWWQRLV 81
           PLRLD G ++  +EIAY+TYG L  D  NA+LICHALTGDQHVASPHP TGKPGWW R+V
Sbjct: 18  PLRLDGGVLLSPVEIAYETYGTLAPDGGNAILICHALTGDQHVASPHPVTGKPGWWTRMV 77

Query: 82  GPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRAQAMLVS 141
           GPGKP+DP RHFI+C+NV+G CMGS+GPA++NPATG+ +G+ FPVITI DMVRAQAML+ 
Sbjct: 78  GPGKPVDPDRHFIVCANVLGSCMGSSGPATVNPATGRPWGMDFPVITIRDMVRAQAMLLD 137

Query: 142 ALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVGRQAIMA 201
            LGV  L AVVGGSMGGMQ   W   +P+R+ + VV+AS +RHSAQNIAFHEVGRQA+MA
Sbjct: 138 HLGVGRLKAVVGGSMGGMQALSWPATFPDRVDAVVVIASTARHSAQNIAFHEVGRQAVMA 197

Query: 202 DPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQ-RDGLSWGFDADFQ 260
           DP W GGAY + G  P  GLAVARMAAHITYLSE  L  KFGR LQ R+  S+GFDADFQ
Sbjct: 198 DPRWNGGAYYD-GDPPAAGLAVARMAAHITYLSEAGLTEKFGRRLQAREAKSFGFDADFQ 256

Query: 261 VESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRARNVRFCVLSFSS 320
           +ESYLRHQG SFVDRFDAN+YLYITRAMDYFD+A  HGG+LA AF   R  RFC++SF +
Sbjct: 257 IESYLRHQGLSFVDRFDANAYLYITRAMDYFDLAEEHGGLLANAFRETR-ARFCLVSFDT 315

Query: 321 DWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFL 372
           DWLYPT ++R +V AL AAGA  +F E+ S  GHDAFLL+ P ++  ++GFL
Sbjct: 316 DWLYPTRDSRAIVHALNAAGAPVSFVELSSPFGHDAFLLEAPELNRVVDGFL 367


Lambda     K      H
   0.321    0.135    0.417 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 540
Number of extensions: 27
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 382
Length of database: 371
Length adjustment: 30
Effective length of query: 352
Effective length of database: 341
Effective search space:   120032
Effective search space used:   120032
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate Ga0059261_2301 Ga0059261_2301 (homoserine O-acetyltransferase (EC 2.3.1.31))
to HMM TIGR01392 (metX: homoserine O-acetyltransferase (EC 2.3.1.31))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01392.hmm
# target sequence database:        /tmp/gapView.11308.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01392  [M=351]
Accession:   TIGR01392
Description: homoserO_Ac_trn: homoserine O-acetyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.7e-145  469.3   0.0   4.4e-145  469.1   0.0    1.0  1  lcl|FitnessBrowser__Korea:Ga0059261_2301  Ga0059261_2301 homoserine O-acet


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Korea:Ga0059261_2301  Ga0059261_2301 homoserine O-acetyltransferase (EC 2.3.1.31)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  469.1   0.0  4.4e-145  4.4e-145       4     350 ..      18     367 ..      16     368 .. 0.98

  Alignments for each domain:
  == domain 1  score: 469.1 bits;  conditional E-value: 4.4e-145
                                 TIGR01392   4 eltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldts 71 
                                               +l l+ G  ls ve+ay+tyGtl+ ++ Na+l+cHaltg++hva+ +  + k GWW++++Gpg+++d++
  lcl|FitnessBrowser__Korea:Ga0059261_2301  18 PLRLDGGVLLSPVEIAYETYGTLAPDGGNAILICHALTGDQHVASPHPVTGKpGWWTRMVGPGKPVDPD 86 
                                               68999***************************************999877667**************** PP

                                 TIGR01392  72 ryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGm 140
                                               r+f+vc+NvlGsc Gs+gP+++np+tg+p+g +fP++tirD+v+aq++lld+Lgv +l+avvGgS+GGm
  lcl|FitnessBrowser__Korea:Ga0059261_2301  87 RHFIVCANVLGSCMGSSGPATVNPATGRPWGMDFPVITIRDMVRAQAMLLDHLGVGRLKAVVGGSMGGM 155
                                               ********************************************************************* PP

                                 TIGR01392 141 qalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmlal 209
                                               qal w ++ p+rv+++vv+a++ar+saq+iaf+ev rqa+++Dp +n+G y++ + P++GLa+ARm a+
  lcl|FitnessBrowser__Korea:Ga0059261_2301 156 QALSWPATFPDRVDAVVVIASTARHSAQNIAFHEVGRQAVMADPRWNGGAYYDGDPPAAGLAVARMAAH 224
                                               ********************************************************************* PP

                                 TIGR01392 210 ltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargr 278
                                               +tY+se+ l e+fgr+ +++e+ ++ ++++f++esylr+qg +fv+rFdAn+Yl++t+a+d++dla+++
  lcl|FitnessBrowser__Korea:Ga0059261_2301 225 ITYLSEAGLTEKFGRRLQAREAKSFGFDADFQIESYLRHQGLSFVDRFDANAYLYITRAMDYFDLAEEH 293
                                               ********************************************************************* PP

                                 TIGR01392 279 rdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveel 345
                                                + l++a+++++a++++v++++D+l+++++++ +++al+aa++   ++e++s+ GHDaFlle+ +++++
  lcl|FitnessBrowser__Korea:Ga0059261_2301 294 GGLLANAFRETRARFCLVSFDTDWLYPTRDSRAIVHALNAAGAPvsFVELSSPFGHDAFLLEAPELNRV 362
                                               *****************************************99888*********************** PP

                                 TIGR01392 346 irefl 350
                                               ++ fl
  lcl|FitnessBrowser__Korea:Ga0059261_2301 363 VDGFL 367
                                               *9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (351 nodes)
Target sequences:                          1  (371 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 8.98
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis